The New York Police Department, at odds with a civilian oversight board about changes to a rule the police used to delay disciplinary decisions for hundreds of days, has increasingly turned its back on the board’s proposed penalties since the rule was tightened.

The police commissioner, James P. O’Neill, is now reducing or rejecting the Civilian Complaint Review Board’s disciplinary recommendations in a substantial majority of cases, even though the board is pursuing more lenient penalties, according to an annual report the board released on Thursday.

By that measure, relations between the two agencies — inherently contentious — are at their lowest point since Mayor Bill de Blasio took office in 2014.

The department’s treatment of review board recommendations last year reversed a yearslong trend as the police made more use of so-called reconsideration requests, a practice allowing the department to challenge the board’s findings or proposed penalties.

But the board, stung by the 200-plus days it was taking the department to lodge such challenges, instituted a 90-day deadline at the end of 2016, with exceptions only for new evidence or a misapplication of the law.

With that change, two years of relative comity between the agencies ended, just a few months into the tenure of Mr. O’Neill, who had succeeded William J. Bratton as commissioner.

In the most serious cases, prosecuted by the review board before a police administrative judge, Mr. O’Neill departed from the board’s recommended penalties 73 percent of the time last year, in most instances after an administrative judge found an officer not guilty. That was up from 60 percent of those cases in 2016.

Overall, almost half of the most serious cases that were closed in 2017 ended with no discipline. And on four occasions, Mr. O’Neill reversed a guilty verdict at trial.

He also broke from the board’s proposed penalties in almost 60 percent of cases in which the board recommended a lower class of penalties last year, up from 34 percent of those cases in 2016.

Richard D. Emery, chairman of the oversight board from 2014 to 2016, said: “The C.C.R.B. very quickly becomes irrelevant because it’s no longer a meaningful part of the disciplinary process, and is just a palliative to people who complain with no real consequence.”

The Police Department has rejected the recommendations of the review board even as the board pursues lighter penalties. The board sought the most serious punishment, which leads to a trial process, against only 11 percent of officers with a substantiated allegation last year, down from 66 percent of such officers in 2013. Instead, the board is more often recommending “command discipline,” which can mean anything from the officer’s getting guidance from a commanding officer to the officer’s forfeiting up to 10 vacation days.

Review board officials have said a 2014 expansion of their disciplinary options allowed them to tailor proposed penalties to an officer’s conduct. Mr. Emery has also said reducing proposed penalties was meant to persuade the police to accept more of the board’s recommendations.

But at the same time, the police started channeling their disagreement into reconsideration requests in 2014. By the second half of 2016, the police took an average of 264 days to lodge a challenge, severely prolonging cases.

Some critics have always said that process was needlessly accommodating of a department that already controlled final outcomes. The police commissioner has the final say over all verdicts and penalties.

The review board tightened its rules further in February, giving the police 30 days to challenge recommendations, with some exceptions.

Kevin S. Richardson, the deputy commissioner in charge of the department advocate’s office, which reviews the oversight board’s recommendations, said police officials had met with the board to express concerns about no longer having enough time to launch challenges. He said the department had added lawyers to the unit that reviews oversight board cases to reduce delays.

In around half the cases of officers who had allegations reconsidered in 2015 and 2016, the review board downgraded the disposition or disciplinary recommendation, and Mr. Richardson said the department would not have broken with the review board so often in 2017 had that trend continued. Last year the board rejected departmental challenges in cases involving 119 officers, stuck with its decisions for 13 officers and downgraded the finding or the disciplinary recommendation for 14.

“Police Commissioner O’Neill is not in any way disregarding or ignoring the C.C.R.B. or not giving them the legitimacy the agency deserves,” Mr. Richardson said.

A growing supply of video evidence has helped the review board close more investigations and substantiate more of those cases. But overall, only a third of cases resolved last year were fully investigated, with many of them truncated because a complainant or witness stopped cooperating or couldn’t be found. People often have to come to the review board’s offices in Lower Manhattan during business hours for a complaint to proceed.

Christopher T. Dunn, the associate legal director for the New York Civil Liberties Union, said the truncation rates were a significant concern: “If you’re a victim of police misconduct, that’s not going to give you a lot of confidence in the C.C.R.B.,” he said.

Jonathan Darche, executive director of the review board, said making the review board more accessible to the public was a priority, with the goal of enabling the agency “to investigate misconduct, identify trends, and ultimately, increase accountability and improve police-community relations.”

A version of this article appears in print on , on Page A23 of the New York edition with the headline: Low Ebb for Relations Between Police and Civilian Oversight Board. Order Reprints | Today’s Paper | Subscribe